Characterization of a novel transitional group Rickettsia species (Rickettsia tillamookensis sp. nov.) from the western black-legged tick, Ixodes pacificus

Rickettsia rickettsii RoaM negatively regulates expression of a limited number of rickettsial genes

The recently described rickettsial protein RoaM (regulator of actin-based motility) negatively regulates the production of actin tails, and its abrogation induces hyper-spreading behavior in many laboratory-adapted strains of Rickettsia rickettsii. RoaM is not surface exposed; thus, its mechanism of regulating actin-based motility is unclear. Using R. rickettsii strains derived from the virulent Sheila Smith strain that express varying levels of roaM, an RNA-seq experiment was performed. We found that roaM-overexpressing strains downregulate expression of at least six genes which may link the regulatory effects of RoaM to the phenotypic effect on motility. Genes regulated by RoaM were confirmed by RT-qPCR. Among the genes regulated is the secreted effector RarP2, which disrupts the trans-Golgi network. Two of the hypothetical proteins were shown to be secreted via fusion to a glycogen synthase kinase tag, which when phosphorylated reveals exposure to the host-cell cytosol. Taken together, these data support the hypothesis that RoaM affects transcription, downregulating rickettsial genes important for pathogenicity in the mammalian host but which are perhaps otherwise detrimental within the tick vector. To determine how RoaM activity may itself be regulated, we investigated a role of temperature in roaM transcription. RoaM expression itself is not temperature dependent, but many other rickettsial genes are, including some also regulated by RoaM. This suggests that rickettsiae utilize multiple mechanisms to control gene expression in response to environmental signals.

IMPORTANCE

RoaM was previously shown to repress the production of actin tails by unknown mechanisms. The roaM gene is negatively selected for in cell culture resulting in hyper-spreading mutants. This work reveals that rather than specifically regulating motility in Rickettsia rickettsii, a set of rickettsial genes is downregulated that includes the type IV secreted effector, rarP2, as well as two other secreted, putative effectors. Relatively few secreted effectors have been identified in Rickettsia. RoaM appears to be part of a larger biological program encompassing active spreading in mammalian cells and may be a critical component for R. rickettsii to transition from arthropod to mammalian host.

Prevalence of Rickettsia species phylotype G022 and Rickettsia tillamookensis in Ixodes pacificus nymphs and adults from Northern California

Ticks are known vectors of various pathogenic bacteria, including species of Rickettsia. Two novel Rickettsia species have been identified in adult Ixodes pacificus: Rickettsia species phylotype G022 in 2011 and R. tillamookensis in 2021. Currently, the pathogenic potential of these species found in I. pacificus remains unknown. This study aimed to determine the prevalence of phylotype G022 and R. tillamookensis in I. pacificus nymphs across different mean annual temperature and relative humidity zones in California. Adult ticks were also tested for phylotype G022. Ticks were collected from multiple locations in seven northern California counties and tested by real-time PCR. The overall prevalence of phylotype G022 and R. tillamookensis in nymphs (n = 550) was 5.3 % (95 % CI = 3.7 %-7.5 %) and 1.6 % (95 % CI=0.8 %-3.3 %), respectively. The overall prevalence of phylotype G022 in adult I. pacificus (n = 720) was 9.0 % (95 % CI = 7.2 %-11.3 %). Phylotype G022 infects nymphal I. pacificus across a broad geographic range. The prevalence of phylotype G022 was higher in the 11.7-13.3 °C (53-56°F) temperature zone, at 6.4 % (95 % CI = 4.5 %-9.2 %), compared to the 13.9-15 °C (57-59°F) zone, where the prevalence was 0.8 % (95 % CI = 0.2 %-4.6 %). In contrast, the prevalence of R. tillamookensis did not show a statistically significant difference between the two temperature zones, with 1.9 % (95 % CI = 0.9 %-4.1 % in the 11.7-13.3 °C (53-56°F) zone and 0.9 % (95 % CI = 0.2 %-4.9 %) in the 13.9-15 °C (57-59°F) zone. The detection of phylotype G022 in both questing nymphs and adults of I. pacificus suggests that it is transmitted transstadially. qPCR testing revealed no coinfections of G022 and R. tillamookensis in any of the nymphs. Although R. tillamookensis exhibited a lower overall prevalence in nymphs compared to phylotype G022, both bacteria exhibited a similar geographic distribution.

Molecular identification and antibiotic clearance of Mycoplasma arginini and Mycoplasma orale from cell cultures infected with Rickettsia or Ehrlichia species

Mycoplasma (Class: Mollicutes) contamination in cell cultures is a universal concern for research laboratories. Some estimates report contamination in up to 35% of continuous cell lines. Various commercial antibiotic treatments can successfully decontaminate clean cell lines in vitro; however, in vitro decontamination of bacterial cultures remains challenging. Intracellular bacteria like those in the genera Rickettsia and Ehrlichia require cell culture for primary isolation and propagation and are thus vulnerable to contamination with mycoplasmas. Some analyses have reported successful antibiotic clearance of contaminating mycoplasmas in Rickettsia cultures; however, many of these studies do not identify the contaminating mycoplasma species and often include only a few isolates. To our knowledge, there are no published studies reporting decontamination of mycoplasmas from Ehrlichia cultures. In this study, we developed a specific multiplex assay to identify two of the most common mycoplasma culture contaminants, Mycoplasma arginini and Mycoplasma orale, in cell cultures infected with Rickettsia or Ehrlichia species. We further describe the successful in vitro decontamination of M. arginini, M. orale, and co-contaminations with both mycoplasmas from multiple Rickettsia and Ehrlichia cultures using daptomycin and clindamycin.IMPORTANCEMycoplasma contamination is a frequent problem in bacterial cell culture. These prolific organisms thrive in the extracellular environment in vitro and can persist in cell lines indefinitely without treatment. Historically, mycoplasma-contaminated Rickettsia cultures were cleared of contaminants by inoculating laboratory mice and re-isolating mycoplasma-free Rickettsia from brain endothelial cells. However, this method requires the sacrifice of live animals and is not always effective. Mycoplasma clearance via mouse inoculation requires a patent infection of murine central nervous system endothelial cells, which may not occur with some mildly pathogenic or nonpathogenic rickettsial species. In vitro antibiotic treatment represents an alternate method to eliminate contaminating mycoplasmas from rickettsial cultures. This method requires minimal adjustment of laboratories that already maintain rickettsial cultures and is not dependent on the use of laboratory animals. As such, the comprehensive strategy for Mycoplasma arginini and Mycoplasma orale elimination presented here can improve laboratory efficiency for in vitro research with intracellular bacteria.

Comparison of transcriptomic profiles between intracellular and extracellular Bartonella henselae

The Bartonella genus of bacteria encompasses ubiquitous species, some of which are pathogenic in humans and animals. Bartonella henselae, the causative agent of Cat Scratch disease, is responsible for a large portion of human Bartonella infections. These bacteria can grow outside of cells, replicate in erythrocytes and invade endothelial and monocytic cells. We have previously reported reduced antibiotic susceptibility of intracellular Bartonella. In this study we performed comparative transcriptomic analyses between the extracellular and intracellular B. henselae phenotypes. Overall, specific genes involved in invasion, virulence, extracellular adhesion of type 4 secretion system were downregulated following intracellular invasion of B. henselae. Downregulation included BadA, a well-characterized adhesin molecule, of critical importance for cell invasion. These studies demonstrate the ability to purify Bartonella RNA from infected cells and offer a repository of gene expression data for future research. The development of novel therapeutics will benefit from the ability to determine target expression by Bartonella in relevant microenvironments.

The roles of habitat isolation, landscape connectivity and host community in tick-borne pathogen ecology

Habitat loss and forest fragmentation are often linked to increased pathogen transmission, but the extent to which habitat isolation and landscape connectivity affect disease dynamics through movement of disease vectors and reservoir hosts has not been well examined. Tick-borne diseases are the most prevalent vector-borne diseases in the United States and on the West Coast, Ixodes pacificus is one of the most epidemiologically important vectors. We investigated the impacts of habitat fragmentation on pathogens transmitted by I. pacificus and sought to disentangle the effects of wildlife communities and landscape metrics predictive of pathogen diversity, prevalence and distribution. We collected pathogen data for four co-occurring bacteria transmitted by I. pacificus and measured wildlife parameters. We also used spatial data and cost-distance analysis integrating expert opinions to assess landscape metrics of habitat fragmentation. We found that landscape metrics were significant predictors of tick density and pathogen prevalence. However, wildlife variables were essential when predicting the prevalence and distribution of pathogens reliant on wildlife reservoir hosts for maintenance. We found that landscape structure was an informative predictor of tick-borne pathogen richness in an urban matrix. Our work highlights the implications of large-scale land management on human disease risk.

Genetic diversity and prevalence of emerging Rickettsiales in Yunnan Province: a large-scale study

BACKGROUND

Rickettsia and related diseases have been identified as significant global public health threats. This study involved comprehensive field and systematic investigations of various rickettsial organisms in Yunnan Province.

METHODS

Between May 18, 2011 and November 23, 2020, field investigations were conducted across 42 counties in Yunnan Province, China, encompassing small mammals, livestock, and ticks. Preliminary screenings for Rickettsiales involved amplifying the 16S rRNA genes, along with additional genus- or species-specific genes, which were subsequently confirmed through sequencing results. Sequence comparisons were carried out using the Basic Local Alignment Search Tool (BLAST). Phylogenetic relationships were analyzed using the default parameters in the Molecular Evolutionary Genetics Analysis (MEGA) program. The chi-squared test was used to assess the diversities and component ratios of rickettsial agents across various parameters.

RESULTS

A total of 7964 samples were collected from small mammals, livestock, and ticks through Yunnan Province and submitted for screening for rickettsial organisms. Sixteen rickettsial species from the genera Rickettsia, Anaplasma, Ehrlichia, Neoehrlichia, and Wolbachia were detected, with an overall prevalence of 14.72%. Among these, 11 species were identified as pathogens or potential pathogens to humans and livestock. Specifically, 10 rickettsial organisms were widely found in 42.11% (24 out of 57) of small mammal species. High prevalence was observed in Dremomys samples at 5.60%, in samples from regions with latitudes above 4000 m or alpine meadows, and in those obtained from Yuanmou County. Anaplasma phagocytophilum and Candidatus Neoehrlichia mikurensis were broadly infecting multiple genera of animal hosts. In contrast, the small mammal genera Neodon, Dremomys, Ochotona, Anourosorex, and Mus were carrying individually specific rickettsial agents, indicating host tropism. There were 13 rickettsial species detected in 57.14% (8 out of 14) of tick species, with the highest prevalence (37.07%) observed in the genus Rhipicephalus. Eight rickettsial species were identified in 2375 livestock samples. Notably, six new Rickettsiales variants/strains were discovered, and Candidatus Rickettsia longicornii was unambiguously identified.

CONCLUSIONS

This large-scale survey provided further insight into the high genetic diversity and overall prevalence of emerging Rickettsiales within endemic hotspots in Yunnan Province. The potential threats posed by these emerging tick-borne Rickettsiales to public health warrant attention, underscoring the need for effective strategies to guide the prevention and control of emerging zoonotic diseases in China.

Metagenome diversity illuminates the origins of pathogen effectors

Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.

Nanopore-based metagenomics reveal a new Rickettsia in Europe

Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum.

Rickettsial Infection in Ticks from a National Park in the Cerrado Biome, Midwestern Brazil

This study was carried out from February 2020 to September 2021 in Parque Nacional das Emas (PNE), a national park located in the Cerrado biome, midwestern Brazil, as well as in surrounding rural properties. Serum and tick samples were collected from dogs, terrestrial small mammals, and humans. Ticks were also collected from the environment. Dogs were infested with Rhipicephalus linnaei adults, whereas small mammals were infested by immature stages of Amblyomma spp., Amblyomma triste, Amblyomma dubitatum, and Amblyomma coelebs. Ticks collected from vegetation belonged to several species of the genus Amblyomma, including A. coelebs, A. dubitatum, Amblyomma naponense, Amblyomma sculptum, and A. triste. Two Rickettsia species were molecularly detected in ticks: Rickettsia parkeri in A. triste from the vegetation and a Rickettsia sp. (designated Rickettsia sp. strain PNE) in A. sculptum and A. triste collected from lowland tapirs (Tapirus terrestris). Based on short gltA gene fragments, this rickettsial organism showed 99.7-100% to Rickettsia tillamookensis. Seroreactivity to Rickettsia antigens was detected in 21.9% of dogs, 15.4% of small mammals, and 23.5% of humans. The present study reveals the richness of ticks and demonstrates the circulation of rickettsial agents in one of the largest conservation units in the Cerrado biome in Brazil. To our knowledge, this is the first report of a rickettsial phylogenetically related to R. tillamookensis in Brazil.

The Ixodes scapularis Symbiont Rickettsia buchneri Inhibits Growth of Pathogenic Rickettsiaceae in Tick Cells: Implications for Vector Competence

Ixodes scapularis is the primary vector of tick-borne pathogens in North America but notably does not transmit pathogenic Rickettsia species. This tick harbors the transovarially transmitted endosymbiont Rickettsia buchneri, which is widespread in I. scapularis populations, suggesting that it confers a selective advantage for tick survival such as providing essential nutrients. The R. buchneri genome includes genes with similarity to those involved in antibiotic synthesis. There are two gene clusters not found in other Rickettsiaceae, raising the possibility that these may be involved in excluding pathogenic bacteria from the tick. This study explored whether the R. buchneri antibiotic genes might exert antibiotic effects on pathogens associated with I. scapularis. Markedly reduced infectivity and replication of the tick-borne pathogens Anaplasma phagocytophilum, R. monacensis, and R. parkeri were observed in IRE11 tick cells hosting R. buchneri. Using a fluorescent plate reader assay to follow infection dynamics revealed that the presence of R. buchneri in tick cells, even at low infection rates, inhibited the growth of R. parkeri by 86-100% relative to R. buchneri-free cells. In contrast, presence of the low-pathogenic species R. amblyommatis or the endosymbiont R. peacockii only partially reduced the infection and replication of R. parkeri. Addition of host-cell free R. buchneri, cell lysate of R. buchneri-infected IRE11, or supernatant from R. buchneri-infected IRE11 cultures had no effect on R. parkeri infection and replication in IRE11, nor did these treatments show any antibiotic effect against non-obligate intracellular bacteria E. coli and S. aureus. However, lysate from R. buchneri-infected IRE11 challenged with R. parkeri showed some inhibitory effect on R. parkeri infection of treated IRE11, suggesting that challenge by pathogenic rickettsiae may induce the antibiotic effect of R. buchneri. This research suggests a potential role of the endosymbiont in preventing other rickettsiae from colonizing I. scapularis and/or being transmitted transovarially. The confirmation that the observed inhibition is linked to R. buchneri's antibiotic clusters requires further investigation but could have important implications for our understanding of rickettsial competition and vector competence of I. scapularis for rickettsiae.

Complete Genome Sequence of Rickettsia parkeri Strain Black Gap

A unique genotype of Rickettsia parkeri, designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus. The compete genome consists of a single circular chromosome with 1,329,522 bp and a G+C content of 32.5%.